Effects of surface tethering on protein folding mechanisms

Proceedings of the National Academy of Sciences of the United States of America

Volumn 103, Issue 22, 2006, Pages 8396-8401

  Friedel, Miriam ^a   Baumketner, Andrij ^a,b   Shea, Joan Emma ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b INSTITUTE FOR CONDENSED MATTER PHYSICS   (Ukraine)

Author keywords

Molecular dynamics simulations; Protein surface interactions; Single molecule spectroscopy

Indexed keywords

MEMBRANE PROTEIN;

ARTICLE; HYDROPHOBICITY; MOLECULAR MECHANICS; NONHUMAN; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN IMMOBILIZATION; PROTEIN LOCALIZATION; PROTEIN PROTEIN INTERACTION; PROTEIN STABILITY; PROTEIN STRUCTURE; SIMULATION; SINGLE MOLECULE SPECTROSCOPY; SPECTROSCOPY;

MODELS, MOLECULAR; PROTEIN DENATURATION; PROTEIN FOLDING; PROTEIN STRUCTURE, TERTIARY; PROTEINS; TEMPERATURE; THERMODYNAMICS;

EID: 33744802398     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0601210103     Document Type: Article

References (46)

1. Schuler, B. (2005) ChemPhysChem 6, 1206-1220.
2. Rasnik, I., McKinney, S. A. & Ha, T. (2005) Acc. Chem. Res. 38, 542-548.
3. Leite, V. B. P., Onuchic, J. N., Stell, G. & Wang, J. (2004) Biophys. J. 87, 3633-3641.
4. Pletneva, E. V., Gray, H. B. & Winkler, J. R. (2005) Proc. Natl. Acad. Sci. USA 102, 18397-18402.
5. Deniz, A. A., Laurence, T. A., Beligere, G. S., Dahan, M., Martin, A. B., Chemla, D.S., Dawson, P. E., Schultz, P. G. & Weiss, S. (2000) Proc. Natl. Acad. Sci. USA 97, 5179-5184.
6. Schuler, B., Lipman, E. A. & Eaton, W. A. (2002) Nature 419, 743-747.
7. Rhoades, E., Gussakovsky, E. & Haran, G. (2003) Proc. Natl. Acad. Sci. USA 100, 3197-3202.
8. Talaga, D. S., Lau, W. L., Roder, H., Tang, J., Jia, Y., DeGrado, W. F. & Hochstrasser, R. M. (2000) Proc. Natl. Acad. Sci. USA 97, 13021-13026.
9. Groll, J., Amirgoulova, E. V., Ameringer, T., Heyes, C. D., Röcker, C., Nienhaus, G. U. & Möller, M. (2004) J. Am. Chem. Soc. 126, 4234-4239.
10. Amirgoulova, E. V., Groll, J., Heyes, C. D., Ameringer, T., Röcker, C., Möller, M. & Nienhaus, G. U. (2004) ChemPhysChem 5, 552-555.
11. Kuzmenkina, E. V., Heyes, C. D. & Nienhaus, G. U. (2005) Proc. Natl. Acad. Sci. USA 102, 15471-15476.
12. Zhuang, X., Bartley, L. E., Babcock, H. F., Russell, R., Ha, T., Herschlag, D. & Chu, S. (2000) Science 288, 2048-2051.
13. Forkey, J. N., Quinlan, M. E., Shaw, M. A., Corrie, J. E. T. & Goldman, Y. E. (2003) Nature 422, 399-404.
14. Rasnik, I., Myong, S., Cheng, W., Lohman, T. M. & Ha, T. (2004) J. Mol. Biol. 336, 395-408.
15. Ha, T., Ting, A. Y., Liang, J., Caldwell, W. B., Deniz, A. A., Chemla, D. S., Schultz, P. G. & Weiss, S. (1999) Proc. Natl. Acad. Sci. USA 96, 893-898.
16. Wazawa, T., Ishii, Y., Funatsu, T. & Yanagida, T. (2000) Biophys. J. 78, 1561-1569.
17. Gray, J. J. (2004) Curr. Opin. Struct. Biol. 14, 110-115.
18. Carignano, M. A. & Szleifer, I. (2002) Mol. Phys. 18, 2993-3003.
19. Tie, Y., Calonder, C. & Van Tassel, P. R. (2003) J. Colloid Interface Sci. 268, 1-11.
20. Raffaini, G. & Ganazzoli, F. (2004) Langmuir 20, 3371-3378.
21. Zhou, J., Tsao, H.-K., Sheng, Y.-J. & Jiang, S. (2004) J. Chem. Phys. 121, 1050-1057.
22. Knotts, T. A., IV, Rathmore, N. & de Pablo, J. J. (2005) Proteins Struct. Funct. Bioinform. 61, 385-397.
23. Shang, J. & Geva, E. (2005) J. Phys. Chem. B 109, 16340-16349.
24. Friedel, M., Sheeler, D. J. & Shea, J.-E. (2003) J. Chem. Phys. 118, 8106-8113.
25. Allen, M. P. & Tildesley, D. J. (1989) Computer Simulation of Liquids (Oxford Univ. Press, Oxford).
26. Zhou, Y., Zhang, C., Stell, G. & Wang, J. (2003) J. Am. Chem. Soc. 125, 6300-6305.
27. Oliveberg, M. (2001) Curr. Opin. Struct. Biol. 11, 94-100.
28. Nymeyer, H., Socci, N. D. & Onuchic, J. N. (2000) Proc. Natl. Acad. Sci. USA 97, 634-639.
29. Fersht, A. R., Matouscheck, A. & Serrano, L. (1992) J. Mol. Biol. 224, 771-782.
30. Shea, J.-E., Onuchic, J. N. & Brooks, C. L., III (2000) J. Chem. Phys. 113, 7663-7671.
31. Vendruscolo, M., Paci, E., Dobson, C. M. & Karplus, M. (2001) Nature 409, 641-645.
32. Hummer, G. (2004) J. Chem. Phys. 120, 516-523.
33. Ding, F., Guo, W., Dokholyan, N. V., Shakhnovich, E. I. & Shea, J.-E. (2005) J. Mol. Biol. 350, 1035-1050.
34. Cho, S. S., Levy, Y. & Wolynes, P. G. (2006) Proc. Natl. Acad. Sci. USA 103, 586-591.
35. Shea, J.-E., Friedel, M. R. & Baumketner, A. (2006) Reviews in Computational Chemistry, eds. Lipkowitz, K. B., Cundari, T. R. & Gillet, V. J. (Wiley-VCH, New York).
36. Du, R., Pande, V. S., Grosberg, A. Y., Tanaka, T. & Shakhnovich, E. I. (1998) J. Chem. Phys. 108, 334-350.
37. Zhu, H. & Snyder, M. (2003) Curr. Opin. Chem. Biol. 7, 55-63.
38. Gō, N. (1983) Annu. Rev. Biophys. Bioeng. 12, 183-210.
39. Kaya, H., Liu, Z. & Chan, H. S. (2005) Biophys. J. 89, 520-535.
40. Honeycutt, J. & Thirumalai, D. (1990) Proc. Natl. Acad. Sci. USA 87, 3526-3529.
41. Guo, Z. & Thirumalai, D. (1995) Biopolymers 36, 83-102.
42. Guo, Z. & Brooks, C. L., III (1997) Biopolymers 42, 745-757.
43. Nymeyer, H., Garćia, A. E. & Onuchic, J. N. (1998) Proc. Natl. Acad. Sci. USA 95, 5921-5928.
44. Shea, J.-E., Nochomovitz, Y. D., Guo, Z. & Brooks, C. L., III (1998) J. Chem. Phys. 109, 2895-2903.
45. Berry, R. S., Elmaci, N., Rose, J. P. & Vekhter, B. (1997) Proc. Natl. Acad. Sci. USA 94, 9520-9524.
46. Klimov, D. K. & Thirumalai, D. (2001) Proteins Struct. Funct. Genet. 43, 465-475.